Aipotu I: Genetics & BiochemistryAipotu I: Genetics & Biochemistry Objectives: • To reinforce your...
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Aipotu I - 1 Aipotu I: Genetics & Biochemistry Objectives: • To reinforce your understanding of Genetics, Biochemistry, and Molecular Biology • To show the connections between these three disciplines • To show how these three approaches can be combined to give a complete picture of a biological phenomenon • To figure out a complete explanation of a biological phenomenon • To experience how scientists develop and test hypotheses Introduction: Aipotu (pronounced “ā pō too“ – the word is “utopia” spelled backwards) is a simulated world where users can explore a biological phenomenon in terms of genetics, biochemistry, molecular biology, and evolution. The Biological Phenomenon Under Study In this lab, you will explore the biological mechanisms behind the expression of flower color in a hypothetical plant. These flowers can be white, red, orange, yellow, green, blue, purple, or black. Scenario: You are the chief biologist for a breeder of fine flowers. Your company sells seeds that customers plant in their gardens. Since most of your customers expect that the flowers will grow each year from seeds produced the previous year, you try to produce true-breeding plants whenever you can. You’ve found a new species of flower with an attractive shape. You’ve collected four plants from the wild: two green, one red, and one white. Your customers would really like to have purple flowers from this plant. You set out to create a true-breeding purple flower. Hypothesis Testing In the three Aipotu labs, you will use a process much like that used by practicing scientists as they conduct research. Although this process almost never follows a formula, it often proceeds as follows: 1. Observe Patterns. Observe the natural world and look for patterns, exceptional events, etc. For example, you might observe that red flowers sometimes have white offspring. 2. Develop hypotheses. From the observations, you define testable hypotheses – statements or questions that can be addressed experimentally. Continuing the example, you might reasonably hypothesize that red is dominant to white. 3. Test hypotheses. You then set up experiments or observations that will collect data that bear on your hypothesis. In the example, you might cross pure-breeding white with pure- breeding red. If your hypothesis is correct, all the offspring will be red. If you get another result, your hypothesis is incorrect. 4. Revise hypotheses as necessary. If your results do not match your prediction, you need to revise your hypothesis and go to Step (3) again until they do match.
Transcript of Aipotu I: Genetics & BiochemistryAipotu I: Genetics & Biochemistry Objectives: • To reinforce your...
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AipotuI:Genetics&BiochemistryObjectives:
• ToreinforceyourunderstandingofGenetics,Biochemistry,andMolecularBiology• Toshowtheconnectionsbetweenthesethreedisciplines• Toshowhowthesethreeapproachescanbecombinedtogiveacompletepictureofa
biologicalphenomenon• Tofigureoutacompleteexplanationofabiologicalphenomenon• Toexperiencehowscientistsdevelopandtesthypotheses
Introduction:Aipotu(pronounced“āpōtoo“–thewordis“utopia”spelledbackwards)isasimulatedworldwhereuserscanexploreabiologicalphenomenonintermsofgenetics,biochemistry,molecularbiology,andevolution.TheBiologicalPhenomenonUnderStudyInthislab,youwillexplorethebiologicalmechanismsbehindtheexpressionofflowercolorinahypotheticalplant.Theseflowerscanbewhite,red,orange,yellow,green,blue,purple,orblack.Scenario:Youarethechiefbiologistforabreederoffineflowers.Yourcompanysellsseedsthatcustomersplantintheirgardens.Sincemostofyourcustomersexpectthattheflowerswillgroweachyearfromseedsproducedthepreviousyear,youtrytoproducetrue-breedingplantswheneveryoucan.You’vefoundanewspeciesofflowerwithanattractiveshape.You’vecollectedfourplantsfromthewild:twogreen,onered,andonewhite.Yourcustomerswouldreallyliketohavepurpleflowersfromthisplant.Yousetouttocreateatrue-breedingpurpleflower.HypothesisTestingInthethreeAipotulabs,youwilluseaprocessmuchlikethatusedbypracticingscientistsastheyconductresearch.Althoughthisprocessalmostneverfollowsaformula,itoftenproceedsasfollows:1. ObservePatterns.Observethenaturalworldandlookforpatterns,exceptionalevents,
etc.Forexample,youmightobservethatredflowerssometimeshavewhiteoffspring.2. Develophypotheses.Fromtheobservations,youdefinetestablehypotheses–statements
orquestionsthatcanbeaddressedexperimentally.Continuingtheexample,youmightreasonablyhypothesizethatredisdominanttowhite.
3. Testhypotheses.Youthensetupexperimentsorobservationsthatwillcollectdatathatbearonyourhypothesis.Intheexample,youmightcrosspure-breedingwhitewithpure-breedingred.Ifyourhypothesisiscorrect,alltheoffspringwillbered.Ifyougetanotherresult,yourhypothesisisincorrect.
4. Revisehypothesesasnecessary.Ifyourresultsdonotmatchyourprediction,youneedtoreviseyourhypothesisandgotoStep(3)againuntiltheydomatch.
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YouhavealreadybeendoingthisinformallyintheVGLlabs.Youshouldnotethatthisprocessneverreallyends–typicallythereismoretoinvestigateonceyou’vereachedasatisfactoryconclusion.The“answer”vsthe“point”Althoughthereisananswer–thecompletemodelofcolorformationintheseplants–andyoucanfinditwiththetoolsinAipotu,havingtheanswerisnotasimportantasfindingtheanswer.Wecouldjusttellyoutheanswer,butthatwouldleaveoutthemajorlearninggoalsofthislab:
• Experiencinghowscientifichypothesistestingworks.• Experiencinghowyoucanusethetoolsofmodernbiologytocompletelyunderstanda
phenomenon.So,whilewewillworktogethertofind‘theanswer’,therealpointofthelabisthejourney.UnifyingThreePartsofModernBiologyThethreemajorpartsofthiscourseare:
• Genetics=explainingbiologicalphenomenaintermsofgenes.Howisflowercolorinherited?
• Biochemistry=explainingbiologicalphenomenaintermsofproteinsandothermolecules.Howdoesproteinsequencedetermineproteinstructureandcolor?
• MolecularBiology=explainingtheconnectionbetweengenes(DNA)andprotein.HowdoestheDNAsequenceofthecolorgeneleadtoaparticularcolor?
TheconnectionsbetweenthesethreefieldsofbiologyareshownbelowinadiagramcreditedtoDavidBotstein(eachofthearrowscorrespondsto“canbeexplainedintermsof”,thewordsinthisfontarethedifferentdisciplinesofbiology): genes individual life functions Molecular oflivingthings Biology proteinsUnderstandinganybiologicalphenomenonrequiresinformationfromallthreeofthesedisciplines.Throughoutthiscourse,youwillre-visitthislabtocreateanincreasinglycompletepictureofthephenomenonunderstudy.Eachtime,youwilladdtothemodelofcolorproductionintheseflowers.GettingAipotu BecauseAipotuisunderconstantdevelopment,youshouldalwaysusethelatestversion.Asaresult,itisnotinstalledonthecomputers.Youshoulddownloaditfromhttp://intro.bio.umb.edu/aipotu/orthelinkontheOn-LineLabManualforthislab.Itwillthenbeinstalledonthedesktop.
Genetics
Biochemistry
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ToolsAvailableinAipotuForeachofthethreedisciplines,thereisadifferenttoolinAipotuthatwillallowyoutoexplorethesamesetofcreaturesusingadifferentsetoftechniques:
• Genetics.Theflowersinthissimulationarediploids.Aswithmostflowers,theyareallhermaphrodites(bothmaleandfemale).Withthistool,youcanperformthefollowingexperiments:
o Crossanytwoorganisms.Anewwindowwillappearwiththeoffspringofthiscross.o Self-crossanyorganism.Inthiscase,thesingleselectedorganismisbothmother
andfathertotheresultingoffspring.o Mutateanyorganism.Anewwindowwillappearwithasetofflowersthatare
mutantversionsoftheselectedorganism.
• Biochemistry.Thecolorintheseflowersresultsfromtheform(s)ofpigmentproteinspresentinanindividualplant.Withthistool,youcanperformthefollowingexperiments:
o Examinethepigmentproteinspresentinaplant.Thetoolshowsyoutheaminoacidsequenceandtwo-dimensionalstructureofthepigmentproteinspresentinagivenplant.
o Designyourownproteins.Youcaneditanexistingproteinsequenceortypeinanentirelynewsequence.Theprogramwillthenpredictthetwo-dimensionalstructureoftheresultingproteinaswellasitscolor.Itwillalsopredictthecolorresultingfromthecombinationofanytwoproteins.
• MolecularBiology.Thepigmentproteinsintheseplantsareproducedbypigmentprotein
genes.Withthistool,youcanperformthefollowingexperiments:o Examinethepigmentproteingenespresentinaplant.ThetoolshowstheDNA,pre-
mRNA,maturemRNA,andproteinsequencespresentinagivenplant.Youcanexploretheintrons,exons,etc.ofthesegenes.
o Designyourowngenes.YoucaneditanexistingDNAsequenceortypeinanentirelynewsequence.TheprogramwillthenpredictthemRNA,proteinsequence,two-dimensionalstructureoftheresultingproteinaswellasitscolor.Itwillalsopredictthecolorresultingfromthecombinationofanytwoproteins.
o Designyourownplants.YoucansaveeditedDNAsequencesasneworganismsforfurtherstudy.
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WhenyoustartAipotu,theprogramwillloadthefourstartingflowertypesintotheGreenhouse,youwillthenseeascreenlikethis:
ThesearetheMenus;theyapplytoallthetools.
TheseButtonsselectthetoolyouwillbeusing.
TheGreenhousecontainsthestartingsetoforganisms.
UpperWorkPanel.Resultsofcrosses,etc.willappearhere.
LowerWorkPanel.Resultsofcrosses,etc.willappearhere.
TheHistoryListstorestheresultsofeachofyourexperiments.Theseresultscanbesenttotheupperorlowerpanes(seelater).
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Eachorganismisshownasaflower:
Thecolorofthepictureshowsthecoloroftheflower.Theseflowerscanbewhite,red,orange,yellow,green,blue,purple,orblack.Whenanyorganismisselected,theblackborderturnsgreentoshowthatithasbeenselected.Thenextsectionsofthismanualwillshowyouthevarioustoolsandthetasksthatyouwillneedtocarryout.PartI:GeneticsTasks:(specificquestionscanbefoundonpages9and10)
• Determinehowcolorisinheritedintheseflowers.NOTE:thecoloriscontrolledbyonegeneonly.
o Determinethecolorsoftheallelespresentintheoriginalsetoforganisms.o Whichallelesaredominant?o Whichallelesarerecessive?o Howdotheallelescombinetoproducetheoverallcoloroftheplant?
• Constructapurpleorganismtodemonstrateyourunderstandingofthisprocess.Usingthetool:Youcanswitchtothistoolbyclickingthe“Genetics”tabnearthetopofthewindow.Therearethreekindsofexperimentsyoucanperformwiththistool.Thefollowingsectionsuseexamplestoshowyouhowtodoeach;youwillneedtodeviseyourownexperimentstocarryoutthetasksabove.I)CrossTwoOrganisms.SupposethatyouwantedtocrossGreen-1andWhite: 1)ClickonGreen-1andthenonWhiteintheGreenhouse.Therectangularbordersof bothshouldturngreentoshowthattheyhavebeenselected.The“CrossTwo Organisms”buttonsintheUpperandLowerWorkPanelsshouldbeactivated.
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2)Clickthe“CrossTwoOrganisms”buttonintheUpperWorkPanel.Youshouldsee somethinglikethis:
Ifyoudouble-clickontheTrayintheHistoryList,yougetapop-upmenuwithalistofusefuloptions:
• SendtoUpperPanel:SendsthisTraytotheUpperPanelsoyoucancrossthoseorganisms.
• SendtoLowerPanel:SendsthisTraytotheLowerPanelsoyoucancrossthoseorganisms.
• AddNotes...:AllowsyoutoaddnotestotheTrayintheHistoryList.ThesenoteswillappearifyouleavethecursorovertheTrayforafewseconds.
• DeletefromHistoryList:deletestheTrayfromtheHistoryList;thisiscannotbeundone.
Thesearetheoffspringofthecross.Youcanselectanyoftheseforcrossing,etc.
ThisrepresentstheTrayofplantscontainingtheoffspringyoujustproduced.Thecoloredsquaresrepresentthedifferentcolorsoftheoffspringproduced.
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II)Self-crossasingleOrganism.Supposethatyouwantedtoself-crossoneoftheoffspringinTray1: 1)SelectanyoneorganismfromTray1intheUpperWorkPanel.Youcande-selectan organismbyclickingonit.Whenyouhaveonlyoneorganismselected,the “CrossTwoOrganisms”buttonswillbegrayedoutandthe“Self-CrossOne Organism”and“MutateOneOrganism”buttonswillbeactivated. 2)Clickthe“Self-CrossOneOrganism”buttonintheLowerWorkPanel.Youshould seesomethinglikethis(sinceoffspringaregeneratedbyrandomchoiceof parentalalleles,youwilllikelyseeslightlydifferentnumbersofredandwhite offspring):Youshouldseesomethinglikethis:
Theoffspringofthisself-crossareintheLowerWorkPanel.NotetheadditionofTray2totheHistoryList.
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Atthispoint,thereareseveralotherthingsyoucando:A)Ifyoufindaninterestingorganism,youcansaveittotheGreenhouse: 1)Clickthe“Add…”buttonatthetopoftheGreenhouse. 2)Youwillbepromptedtogivetheorganismaname.Giveitadescriptivenameand click“OK”.YouwillseeyourneworganismappearintheGreenhouse.You cannowaccessitusingtheothertoolsinthisprogram. 3)Atthispoint,theorganismissavedintheprogram,butnotonthedisk.Tosavethe contentsoftheGreenhousetodisk,clickontheGreenhouseMenuandselect “SaveGreenhouse”.B)YoucancrossormutateanyoftheorganismsvisibleintheGreenhouse,UpperWork Panel,orLowerWorkPanel.C)YoucanbringanyTrayfromtheHistoryListtoaWorkPanelbydouble-clickingtheTrayandselectingtheappropriateiteminthepop-upmenu.D)YoucanaddnotestoanyTrayintheHistoryListbydouble-clickingtheTrayandchoosingthe“AddNotes...”itemfromtheresultingpop-upmenu.ThesenoteswillappearifyouleavethecursorovertheTrayforafewseconds.IMPORTANTNOTE:Thissoftwareisunderdevelopment.Pleasetreatitgentlyandbepatient.PleasereportanybugstoyourTA.YoushouldsaveyourGreenhouseregularly,especiallyifyousavealargenumberoforganisms.SpecificTaskstodowiththistool:
a) Howmanydifferentallelesarethere?Whichcolorsdotheyproduce?Itwillbeusefultousemultiple-allelenotationlikethis:CR=red;CG=green,etc.
b) Whicharedominantandwhicharerecessive?c) Howdothecolorscombinetoproduceanoverallcolor?Forthis,itmayhelptomakea
genotype-phenotypetableandthentrytoabstractrulesfromthat.Youshouldbesurethatyouhavetriedallthepossiblecombinationsoftheallelesyoufoundinpart(a).
d) Usingthesymbolsyouhavedeveloped,givethegenotypesofthefourstartingorganisms.e) Usingthisknowledge,constructapurpleflower.f) Canyouconstructapure-breedingpurpleflowerwiththestartingsetoforganisms?g) Postyourfindingstoyoursection’sLabDataBlog.
HowtogoaboutaccomplishingthesetasksFollowtheprocedurefrompage(1)–lookforpatterns,makehypotheses,testhypotheses,revisehypotheses.Today,wewillnotwritethemoutformally,butyoushouldbethinkinginthesetermsfortheAipotuIIlablaterinthesemester.
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Putyourdatainthetablesbelow:(a)and(b) allele color(c)Genotype PhenotypeWhatrulescanyoufindtoexplainthedataabove?
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(d)Usingtheallelesymbolsabove,whatarethegenotypesofthestartingstrains? Green-1: Green-2: Red: White:(e)HaveyourTAcheckoffthatyouhaveconstructedapurpleflower.Forfullcredit,youmustbeabletoexplaintoyourTAwhytheflowerispurple.(f)Canyouconstructapure-breedingpurpleflowerusingonlythefourstartingstrains?Whyorwhynot?(g)Haveonegrouppostyourresultstoyoursection’sLabDataBlog.
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PartII:BiochemistryITasks:Worktogetherasaclassto:
• Explain,intermsoftheproteinspresent,theinteractionsbetweentheallelesyoufoundinPartI.
o Whyisthecolorphenotypeofsomepigmentproteinsdominantwhileothersarerecessive?
o Howdothepigmentproteinscombinetoproducetheoverallcoloroftheplant?• Determinethedifferencesinaminoacidsequencebetweentheproteinsproducedbythe
allelesyoufoundinPartI.• Begintodeterminehowtheaminoacidsequenceofapigmentproteindeterminesitscolor
–youwillcompletethistaskintheAipotuIIlablaterinthesemester.Asinrealscience,thesetasksaretoobigtobesolvedbyonegroupalone.Ifyouthinkofrealresearchassolvinganenormousjigsawpuzzle,eachresearcherworksononlyonelittlecornerofthepuzzle.Scientistspublishpapersandpresentfindingsatconferencesinordertoconnectthecornersofthepuzzlethateachisworkingon.ImportantNote:Itisalwaysimportanttokeepinmind,the‘scientist’smantra’:alwaysbeaskingyourself“HowcouldIbebeingfooledbythis?”Tocontinuetheexamplefromthepreviouspage,considerthefollowing:Supposethatthelongthinproteinwerered,youmightcongratulateyourselfthatyouhadfoundtheconnectionbetweenshapeandcolor.However,whatiftherealmechanismisthatproteinscontainingarginineareredandyourlongthinproteinjusthappenedtobemadewitharginine.Theredcolorwouldbefoolingyouintothinkingyouhaditright.Howdoyouavoidthistrap?Eventhebestscientistssometimesfallintotrapslikethis.Theansweristoalwaysbethinkingofalternativeexplanationsforyourresults.Inthecaseabove,onelongthinredproteindoesnotmeanthat“long&thin=red”.Youhavetocollectmoredata:proteinsthataren’tlongandthin;longandthinproteinswithdifferentaminoacids;etc.Inthispartofthelab,morethaninthefirstpart,itistheprocessofscienceratherthantheanswerthatismostimportant.Youwilluseablogtocollaborateasaclasstosolvethisscientificproblem.Inthislab,youwilluseaweblogor‘blog’tosharehypotheses,data,andconclusionsamongyourlab-matessothatyoucansolvethisprobleminthethreehoursofthelabperiod.Individualcontributionscanbesmall,orevennegative(“Iknowthatitcan’tbe…”),butyouwillbeabletoaccomplishthetasksaboveifyouworktogether.Inresearch,noone‘owns’data–thepointistofigureouthowtheworldworks,notwhogottheresult.Thisblogwillalsobeavailableonthewebforwhenyouwriteyourlabreports.
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Usingthetool:OnceyoustartAipotu,youcanswitchtothetoolforthissectionbyclickingthe“Biochemistry”tabnearthetopofthewindow.Youwillseesomethinglikethis:
Thispartoftheprogramusestheone-lettercodeforthe20aminoacids:
AminoAcid 3-lettercode
1-lettercode
Mnemonic
Alanine Ala A AlanineArginine Arg R aRginineAsparagine Asn N asparagiNeAsparticacid Asp D asparDicacidCystine Cys C CystineGlutamine Gln Q Q-tamineGlutamicAcid Glu E glu-tE-amicacidGlycine Gly G GlycineHistidine His H HistidineIsoleucine Ile I IsoleucineLeucine Leu L LeucineLysine Lys K lysinKMethionine Met M MethioninePhenylalanine Phe F FenylalanineProline Pro P ProlineSerine Ser S SerineThreonine Thr T ThreonineTryptophan Trp W tWptophanTyrosine Tyr Y tYrosineValine Val V Valine
Thisisareferenceforthenamesandpropertiesoftheaminoacids.• Thesingle-lettercodeisshownbelowthethree-lettercode.• Whitecirclesarehydrophilic;grayareintermediate;andblackare
hydrophobic.• Ared(-)indicatesanegatively-chargedsidechain• Ablue(+)indicatesapositively-chargedsidechain• Agreen(*)indicatesasidechainthatcanmakeahydrogenbond.
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• ClickintheAminoAcidSequenceBoxatthetopoftheUpperFoldingWindow.Typeashortsequenceoflettersandyouwillseeashortaminoacidsequenceappearinthewindow.Thistoolconvertsthesingle-lettercodetothethree-lettercodeautomatically.
• Clickthe“FOLD”buttonandatwo-dimensionalversionofyouraminoacidsequencewillappearintheFoldedProteinwindow.
Thereareseveralimportantthingstonoteaboutthisfoldingprocess:ItisthesameasyouusedintheProteinInvestigator.Thisisahighly-simplifiedmodelofproteinfolding.Itisnotintendedtopredictthecorrectstructuresofanyproteins;itisdesignedtoillustratethemajorprinciplesinvolvedinthatprocess.Theimportantfeaturesofproteinsthatthissoftwareretainsareasfollows:
• Aminoacidshaveside-chainsofvaryinghydrophobicity,charge,andhydrogenbondingcapacity.
• Theaminoacidsareconnectedinanun-branchedchainthatcanbend.• Hydrophobicaminoacidswilltendtoavoidthewaterthatsurroundstheprotein;
hydrophilicaminoacidswillbindtothewater.• Aminoacidsthatcanformhydrogenbondswilltendtoformhydrogenbondsiftheycan.• Positively-chargedaminoacidswilltendtoformionicbondswithnegatively-charged
aminoacidsiftheycan.• Like-chargedaminoacidswillrepeleachotheriftheycan.• Ionicinteractionsarestrongerthanhydrogenbonds,whicharestrongerthanhydrophobic
interactions.Eventhoughthissoftwareprovidessomeimportantinsightsintoproteinfolding,youshouldalwayskeepinmindthatthisisanapproximation.Themostimportant"gotcha's"tobeawareofare:
• Thisprogramfoldsproteinsin2-dimensionsonly.• Thisprogramtreatsallaminoacidsasequal-sizedcircles.• Thisprogrammodelsanenvironmentwheredisulfidebondsdonotform.• Thisprogramfoldstheproteinbasedontheinteractionsbetweenthesidechainsonly.• Thisprogramdoesnotmodelsecondaryorquaternarystructure.• Thisprogramassumesthatallsidechainswithhydrogenbondingcapabilitycanbondwith
eachother.Thesesimplificationsarenecessaryfortworeasons.Thefirstistechnical:itturnsouttobeextremelydifficulttopredictthefull3-dfoldedstructureofaproteingivenonlyitsaminoacidsequence.Asofthewritingofthislabmanual,ittakesasuper-computerseveraldaystopredictthefully-foldedshapeofevenasmallproteinlikelysozyme.Eventhen,thepredictionsdon’talwaysmatchknownstructures.GiventhecomputerswehaveintheBio111labs,itmighttakeyears….Thesecondreasoniseducational.Proteinsarecomplex3-dimensionalmolecules;thus,itcanbehardtofindyourwayaroundwheninsideone.Likewise,itwouldbeverydifficulttovisuallycomparetwoproteinmoleculestoobservetheeffectsofchangestotheiraminoacidsequence.Itwouldbeeasytomisstheforest(theforcesthatcontrolproteinstructure)forthetrees(thetinydetailsofthestructures).
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Forthesereasons,wewillusethissimplification.Itretainsthepropertiesofaminoacidsthatareimportantforthislabwhilebeingsimpleandfast.Therearethreekindsofexperimentsyoucanperformwiththistool.Thefollowingsectionsuseexamplestoshowyouhowtodoeach;youwillneedtodeviseyourownexperimentstocarryoutthetasksfromthepreviouspage.I)ExaminethePigmentProteinsPresentinanOrganismfromtheGreenhouse.Thissimulatesextractingthepigmentprotein(s)producedbythetwoallelesofthepigmentproteingenethatanorganismpossesses,displayingtheirtwo-dimensionalstructures,anddisplayingtheircolors. 1)Double-clickontheGreen-2organismintheGreenhouse.Youshouldseethis:
TheGreenorganismcontainstwoallelesofthepigmentproteingene.Eachoftheseallelesproducesadifferentprotein.OneoftheseproteinsisshownintheUpperFoldingWindow;itisablue-coloredproteinasshownbythebluesquarenexttothe“Color:”label.TheotherproteinisshownintheLowerFoldingWindow;thisisyellow-coloredprotein.ThecombinedcolorofthetwoproteinsisgreenasshownbytheCombinedColorinbetweenthetwoFoldingWindows.II.ExaminingPigmentProteinsFromtheMutantOrganism(s)YouMadeintheAipotuILab.Youcangobacktoyoursection’sLabDataBloganddownloadanysavedorganism(s)tothegreenhouse.Control-clickonthefilenamelinkandselectDownloadLinkedFileAs….NavigatetotheDesktop,intotheAipotufolder,andfinallysaveitintheGreenhousefolder.Ifyounowquitandre-startAipotu,youwillseetheneworganismintheGreenhouse.
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III)Comparetheaminoacidsequencesoftwopigmentproteins.Thisalignsthetwoaminoacidsequencessothatthehighestnumberofmatchingaminoacidsisobtainedandthenfindstheremainingdifferences. 1)Double-clickontheGreen-2organismintheGreenhouse.Youshouldseethatthe UpperFoldingWindowshowsablueproteinandtheLowerFoldingWindow showsayellowprotein. 2)Youcancomparetheaminoacidsequenceofthesetwoproteinsbyclickingonthe “Compare”menuandchoosing“Uppervs.Lower”.Awindowwillappear showingthedifferencesbetweenthetwosequences.Thisisshownbelow:
Thisshowsthattheonlydifferenceisthat,intheupper(blue)protein,aminoacid10is tyrosine,whileinthelower(yellow)protein,aminoacid10istryptophan. ÞYoucanalsocopythesequenceofaparticularproteintotheclipboardusingthe optionsintheEditmenu.YoucanthenCompareasequencetotheoneinthe clipboard.IV)EditaProteinSequenceorCreateaNewProteinSequenceandDetermineitsTwo-DimensionalStructureandColor.YoucaneditthesequenceineitheroftheAminoAcidSequenceboxesandclickthe“Fold”buttontopredictthetwo-dimensionalstructureandcoloroftheprotein.ThetoolwillalsogivethecolorthatresultsfromthecombinationofthecolorsintheUpperandLowerwindows.Forexample,clickanywhereinthe“Tyr”correspondingtoaminoacid10intheUpperAminoAcidSequencebox.Clickthe“delete”keyandthataminoacidwilldisappear.Typean“L”(theonelettercodeforleucine)andtheaminoacidsequenceshouldbe: MetSerAsnArgHisIleLeuLeuValValCysArgGlnClickthe“FOLD”buttonintheUpperFoldingWindow(orclickthereturnkey).Youwillseethatthecolorofthenewproteiniswhiteasshownbythe“Color:”intheUpperFoldingWindow.Youshouldalsonoticethat:
• the“CombinedColor”atthecenterofthewindowisnowyellow.• thereisnowanentryintheHistoryListwithyournewprotein.Thebackgroundof
HistoryListentryiswhitetoshowthecolorofthisprotein.Youcanalsoclickthe“LoadSampleProtein”button.Thiswillloadasampleaminoacidsequencethatfoldstoawhite-coloredproteinwithashapethatissimilartomanycoloredproteins.
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Ifyoudouble-clickanentryintheHistoryList,youwillyougetapop-upmenuwithalistofusefuloptions:
• SendtoUpperPanel:SendsthisTraytotheUpperPanelsoyoucancrossthoseorganisms.
• SendtoLowerPanel:SendsthisTraytotheLowerPanelsoyoucancrossthoseorganisms.
• AddNotes...:AllowsyoutoaddnotestotheTrayintheHistoryList.ThesenoteswillappearifyouleavethecursorovertheTrayforafewseconds.
• DeletefromHistoryList:deletestheTrayfromtheHistoryList;thisiscannotbeundone.
ÞYoucanalsotakeaSnapshotofeitherWorkPanelInordertomakeentriesinthedatablog,youwillneedtotakesnapshotsofparticularproteins.Atypicalsnapshotlookssomethinglikethis;itshowstheprotein’sshape,aminoacidsequence,andcolor:
Youcantakeasnapshotineitheroftwoways:
• Saveasnapshotasapicture.IntheFilemenu,chooseeitherSaveImageofUpperPanel…orSaveImageofLowerPanel….Youwillthenbeaskedtogivethefileanameanditwillbe(typically)savedtothedesktopasname.png;youcanthenimportthatfileintothedatablog.
• Takeasnapshottotheclipboard.IntheEditmenu,chooseeitherCopyImageofUpperPaneltoClipboardorCopyImageofLowerPaneltoClipboard.Youcanthenpastetheresultingimageintoanotherprogram,likeMicrosoftWord.
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UsingtheBlogtocollaborateduringclassThedatablogwillallowallthemembersoftheclasstosharehypotheses,data,andconclusionsinascaled-downscientificcommunity.Asyouwork,youshouldposttotheblog.Youshouldnotpostallyourdata;justtheinterestingbits.Itisprobablybettertoerronthesideofincludingsomethingratherthannot;youneverknowifitwillturnouttobeinteresting.Youshouldalsoconsulttheblogfrequentlytoseeifthereisdatatherethatwillhelpyoufigureoutwhat’sgoingon.Periodically,yourTAwillaskyoutotakeabreaktohaveabriefresearchsymposiumwhereyouwillreviewtheblogasaclassanddiscusswhatyou’vefoundsofarandwhereyoushouldbegoing.Usingtheblogwillbetrickyatfirst,butitwillsoonbecomeeasier.I)LoggingIn–loginthroughyourBlackboardaccountandgototheBio111page.II)Posting–youshoulddothiswhenyouhaveaninterestingresulttosharewiththeclass.Again,itisbettertoerronthesideofpostingthannotposting.Usethefollowingprocedure:1)Clickthe“LabBlogs”linkinthenavigationlist:2)InthelistofLabBlogs,clickonthelinkforyourlabsection.3)Click“CreateBlogEntry”.4)Youwillseesomethinglikethis:
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Apostshouldcontainthefollowingelements:
• Title.EnterthisintheTitlebar.Itshouldcontainyourgroupnameandashortphraseindicatingthesubjectofyourpost.Forexample,“Brian,Tina,&Ling:Thislongproteinisred!”
• AnImageoftheprotein.
o First,savetheimagetothedesktop.UsingAipotu’s“SaveImageof…Panel…”fromtheFilemenu,saveanimageoftheinterestingproteintotheDesktop.Giveitadistinctivenamesoyoucanfinditeasily.Aipotuwilladd“.png”totheendofthefilenametocorrectlyidentifyitasanimage.
o Next,insertitintothepost.Usethe“Insert/EditImage”button.DONOTUSEthe“AttachFile”buttons.
• AHypothesis.Usingtheformatbuttons,selectboldtypeandtype“Hypothesis:”.Gotothe
nextlineand,usingregulartype,writethehypothesisyouwereexploring.Forexample,“Longthinproteinswillbered”.
• TheExperiment.“Experiment:”shouldbeboldandonit’sownline.Followwithabrief
descriptionoftheexperiment;forexample,“Wedesignedalongthinprotein”.
• TheResult.“Result:”shouldbeboldandonit’sownline.Followwithabriefstatementdescribingtheresult;forexample,“Theproteinwascolorless”.
• TheConclusion.“Conclusion:”shouldbeboldandonit’sownline.Followwithabrief
conclusion;inthiscase,“Thehypothesisisincorrect;longthinproteinsarenotnecessarilyred.”
Titlebar
Insertpicturebutton(USETHISONE)
Dangerdanger!(Donotusethisbutton)
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ASamplepost:
IMPORTANTNOTES:(1)Thissoftwareisunderdevelopment.Pleasetreatitgentlyandbepatient.PleasereportanybugstoyourTA.YoushouldsaveyourGreenhouseregularly,especiallyifyousavealargenumberoforganisms.Youshouldalsopostpicturestotheblogassoonasyoucan.(2)Don’tshutdownorrestartthecomputeroryouwillloseallthepicturesyou’vesavedontheDesktopandalltheorganismsyou’vesavedintheGreenhouse.SpecificTasksforthissectionWorkasaclass,usingthedatablogto:
a) WhatarethedifferencesintheaminoacidsequencesoftheproteinsproducedbytheallelesyoudefineinPartI?Hint:usetheComparemenutofindthedifference(s)betweentheaminoacidsequences.
b) Howdothecolorscombinetoproduceanoverallcolor?Howdoesthisexplainthegenotype-phenotyperulesyoufoundinPartI?
c) Starttoworkonthese;postpreliminaryfindingsandquestionstolabblog.Youwillfinishthislaterinthesemester:
o Whatfeaturesoftheaminoacidsequencemakeaproteinpigmented?o Whatfeaturesoftheaminoacidsequencemakeaproteinaparticularcolor?o Whichproteinsarefoundineachofthefourstartingorganisms?o Usingthisknowledge,constructapurpleprotein.
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Hints:A) Itmaybeuseful,beforeformulatinganyhypotheses,tolookforpatternsinthedata.
Whichfeaturesdocoloredproteinshaveincommonthatuncoloredproteinslack?• Trycomparingtheaminoacidsequencesofproteinswithdifferentcolors.• Herearesomeadditionalinterestingsequencestotry:
• FFFFFFFRRRRRR• RRRFFFFFFFRRR• KKKKKKLLLLLLF• KKKKKKLLLLLLL• SLQLNITMEVDFW• EEEWWWWWWWEEE
B) Scientists,includingyourselves,oftenfinditusefultousemutationtostudyphenomena
likethis.GotoGeneticsandmakesomemutants.SaveanyoneswithinterestingcolorstotheGreenhouse.SwitchbacktoBiochemistryandlookattheproteinstheyhave.
Procedure:
1. Comparetheproteinsfoundinthestartingstrainstoanswerquestions(a)and(b)onthefollowingpages.
2. YourTAwillassignyourgrouponeparticularcoloredproteintostudy.Compareitssequenceandshapetothe“sampleprotein”thatyougetbyclickingtheLoadSampleProteinbuttonononeoftheFoldingWindowsandthenchoosingfromtheComparemenu.
3. Arepresentativefromeachgroupwillcometotheboardtodescribethesequenceand
shapedifference(s)betweentheirproteinandthesample.Notethateachsubsequentgroupshouldrelatetheirfindingstothepreviously-presenteddata.
4. Basedonthesedata,asaclass,makeseveralspecifichypothesesthatcanbetested.
5. Eachgroupshouldworkononeormoreoftheirhypothesesandpostthemtotheblog.
6. YourTAmaystopforamini-symposiumtosharedataanddesignnewhypotheses.
7. Youwillthenbeabletocompleteparts(d)through(f).
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Putyourdatainthetablesbelow:(a)Whichproteinsarefoundineachofthefourstartingorganisms? Green-1 Green-2 Red White(b)allele color aminoacidsequence(highlightdifferences)Wewillstarttoworkonthesequestionstoday.WewillrevisitandfinishthemintheAipotuIIlablaterinthesemester.Besuretotakegoodnotesandposttothelabblogtokeeparecordofyourthoughts,conclusions,andquestions.(c)Whatfeaturesofaproteinmakeitcolored?
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(d)Whatfeaturesoftheaminoacidsequencemakeaproteinaparticularcolor?(e)Howdothecolorscombinetoproduceanoverallcolor?Howdoesthisexplainthegenotype-phenotyperulesyoufoundinpart(I)?(f)ShowyourTAthatyouhavemadeapurpleprotein.Forfullcredit,youneedtoexplaintoyourTAwhyitispurple.
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Labreport• Mustbetyped;handwrittenreportswillnotbeaccepted.• Dueduringtheweeklistedinthesyllabusatthestartofthelabsessionyouarecurrentlyin.
Thisisafirmdeadline.• Althoughyouwillperformtheseexperimentsasagroup,eachmemberofthegroupmustturn
inanindividuallabreportandthisreportmustbeinyourownwords.Yourlabreportmustinclude:Adescriptionofoneplacewhereonehypothesis(abouttherelationshipbetweensequence,structure,andcolor)andsomedatainteractedtoleadtoafirmconclusion.NotethatthehypothesismustbefromtheBiochemistrysectionofthislab.Youshouldnotdescribealltheexperimentsyoudid;justoneplacewhereyouwereabletodrawafirmconclusion.Theconclusioncanbepositive(“Myhypothesiswassupportedbecause…”)ornegative(“Myhypothesiswasnotsupportedbecause…”).Thisneednotbeanexperimentyoudid,butitmusthavehappenedduringyourlabsession.1)Hypothesis–thehypothesisbeingtested.Youmustpickaclearandspecifichypothesisthatcanbeclearlyanddecisivelytestedbytheexperiment(s)youdescribebelow.Yourhypothesisneednotbecorrect.2)Experiments–adescriptionoftheexperiment(s)youtriedthataddressedthehypothesis.Donotincludeallyourexperiments;onlythoserelevanttothehypothesisfrompart(1).Thesemustclearlyanddecisivelytestyourhypothesis.3)Results–picturesoftheresultsoftheexperiments.Youcangetthesefromyoursection’sblogpage.Justdragthepicturefromthewebpagetothewordprocessor.Youmayneedtonotethecolor(s)intextsincemostprintersprintinblackandwhite.4)Conclusions–dothedatasupportthehypothesisornot.Explainyourreasoning.Youwillbegradedonthequalityofyourargument:howclearlyyoudescribedyourhypothesis,experiment(s),andresult(s)aswellashowclearlyandcompletelyyourconclusionsareexplained.
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